MUCOSA-ASSOCIATED MICROBIOME IN INDIAN PATIENTS WITH ULCERATIVE COLITIS IS DYSBIOTIC, ENRICHED WITH PRO-INFLAMMATORY PATHOBIONTS, AND CHARACTERIZED BY AN ELEVATED FIRMICUTES/BACTEROIDETES RATIO

Abstract BACKGROUND Ulcerative colitis (UC) is a chronic inflammatory bowel disease driven by complex interactions between genetics, environment, and the gut microbiota, with rising incidence in developing nations. India, currently in stage 2 of the IBD epidemiological transition, reports one of the highest case burdens in Southeast Asia. While gut microbial dysbiosis is implicated in UC pathogenesis, most studies have focused on fecal microbiota, with limited exploration of the mucosa-associated microbiome (MAM), which resides in close contact with the intestinal epithelium. This study aimed to characterize microbial signatures relevant to UC pathogenesis in Indian patients, where high fecal–oral transmission and infection rates may uniquely shape microbial dynamics. METHODS The microbiomes of colonic mucosal biopsies were characterized from 30 patients with established UC (inflamed areas) and 30 non-IBD controls (normal mucosa). DNA was extracted using a mechanical–chemical lysis protocol followed by kit-based purification. V3–V4 region of 16S rRNA gene was sequenced on the Illumina MiSeq platform (2 × 300 bp). Data were processed using the DADA2 pipeline, followed by taxonomic assignment with the SILVA database. Diversity analyses (alpha and beta), phylum-level comparisons, LEfSe-based biomarker discovery, species-level differential abundance testing, and Spearman correlation-based co-occurrence network analysis were conducted to assess the microbial communities in UC. RESULTS UC samples showed significantly altered beta diversity across all taxonomic levels and a notably elevated Firmicutes-to-Bacteroidota ratio (mean 1.91). Enrichment of Firmicutes and Desulfobacterota, alongside reduction of Fusobacteriota, Actinobacteriota, Patescibacteria, and Spirochaetota, characterized the UC microbiome. LEfSe revealed UC-associated families such as Campylobacteraceae, Lachnospiraceae, and Cardiobacteriaceae, while Porphyromonadaceae, Spirochaetaceae, and Actinomycetaceae were enriched in controls. At the species level, pathobionts including Bacteroides fragilis, Parabacteroides goldsteinii, Escherichia sp., and Campylobacter concisus were elevated in UC, whereas health-associated commensals like Streptococcus infantis, Capnocytophaga spp., and Lactobacillus casei were reduced. Network analysis revealed strong positive correlations among pro-inflammatory taxa in UC, indicating tightly clustered microbial communities potentially driving mucosal inflammation. CONCLUSIONS Our findings highlight distinct mucosal bacterial signatures in Indian patients with UC, marked by enrichment of pro-inflammatory pathobionts, depletion of beneficial commensals, and an increased Firmicutes-to-Bacteroidota ratio. These results underscore the importance of region-specific MAM profiling and support the integration of microbial signatures into personalized treatment strategies for UC.